Mnemiopsis leidyi genomic resources and raw data

• Mnemiopsis genome portal

• 454 reads used in the Mnemiopsis leidyi genome assembly (Ryan et al. 2013)

• Genome Analyzer IIx reads used in the Mnemiopsis leidyi genome assembly (Ryan et al. 2013)

• Illumina Mi-Seq run used to estimate heterozygosity in the 2013 genome paper (Ryan et al. 2013)
        Note: these are from a different Woods Hole sample than the one used in the assembly
        Note: these reads were aligned to the assembly and then samtools was used to generate fastq files from the bam file (hence the 747,235 unpaired reads).
        The R1 and R2 files have 139,013,990 reads. Each read is 101 nucleotides
  • Mlei.miseq.R1.fq.gz
  • Mlei.miseq.R2.fq.gz
  • Mlei.miseq.unpaired.fq.gz

• mixed-stage embryo RNA-Seq used to annotate the Mnemiopsis leidyi genome (Ryan et al. 2013)
  • SRA FASTQ Single-end RNA-Seq data from Mnemiopsis leidyi
  • SRA FASTQ Paired-end RNA-Seq data from Mnemiopsis leidyi

• Small RNA reads used in Maxwell et al. (2012)
  • SRA FASTQ Libraries of small RNAs sample 1
  • SRA FASTQ Libraries of small RNAs sample 2

• RNA-Seq from tentacle bulbs used in Babonis et al. (2018)
  • SRA FASTQ Tentacle bulb BULK RNA-Seq sample 1
  • SRA FASTQ Tentacle bulb BULK RNA-Seq sample 2
  • SRA FASTQ Tentacle bulb BULK RNA-Seq sample 3

• RNA-Seq from Comb Rows used in Babonis et al. (2018)
  • SRA FASTQ Comb row BULK RNA-Seq sample 1
  • SRA FASTQ Comb row BULK RNA-Seq sample 2
  • SRA FASTQ Comb row BULK RNA-Seq sample 3

  References

  Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Integrating Embryonic Development and Evolutionary History to Characterize Tentacle-Specific Cell Types in a Ctenophore. Mol Biol Evol. 2018 Dec 1;35(12):2940-2956. doi:10.1093/molbev/msy171

  Maxwell EK, Ryan JF, Schnitzler CE, Browne WE, Baxevanis AD. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics. 2012 Dec 20;13:714. doi:10.1186/1471-2164-13-714

  Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013 Dec 13;342(6164):1242592. doi:10.1126/science.1242592